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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:10:02 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 longitudinal nmit" id="qiime2__longitudinal__nmit" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Nonparametric microbial interdependence test</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version longitudinal</version_command>
19 <command detect_errors="aggressive">q2galaxy run longitudinal nmit '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[RelativeFrequency]" help="[required] Feature table to use for microbial interdependence test.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator>
29 </param>
30 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">
31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
32 <param name="type" type="select" label="metadata: Metadata">
33 <option value="tsv" selected="true">Metadata from TSV</option>
34 <option value="qza">Metadata from Artifact</option>
35 </param>
36 <when value="tsv">
37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
38 </when>
39 <when value="qza">
40 <param name="source" type="data" format="qza" label="Metadata Source"/>
41 </when>
42 </conditional>
43 </repeat>
44 <param name="individual_id_column" type="text" label="individual_id_column: Str" help="[required] Metadata column containing IDs for individual subjects.">
45 <sanitizer>
46 <valid initial="string.printable"/>
47 </sanitizer>
48 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
49 </param>
50 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
51 <param name="corr_method" type="select" label="corr_method: Str % Choices('kendall', 'pearson', 'spearman')" display="radio">
52 <option value="kendall" selected="true">kendall</option>
53 <option value="pearson">pearson</option>
54 <option value="spearman">spearman</option>
55 </param>
56 <param name="dist_method" type="select" label="dist_method: Str % Choices('fro', 'nuc')" display="radio">
57 <option value="fro" selected="true">fro</option>
58 <option value="nuc">nuc</option>
59 </param>
60 </section>
61 </inputs>
62 <outputs>
63 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
64 </outputs>
65 <tests/>
66 <help>
67 QIIME 2: longitudinal nmit
68 ==========================
69 Nonparametric microbial interdependence test
70
71
72 Outputs:
73 --------
74 :distance_matrix.qza: The resulting distance matrix.
75
76 |
77
78 Description:
79 ------------
80 Perform nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. For more details and citation, please see doi.org/10.1002/gepi.22065
81
82
83 |
84
85 </help>
86 <citations>
87 <citation type="doi">10.1002/gepi.22065</citation>
88 <citation type="doi">10.1128/mSystems.00219-18</citation>
89 <citation type="doi">10.1038/s41587-019-0209-9</citation>
90 </citations>
91 </tool>